The Child is Lost
by TheStarShines
Summary: The Doctor hasn't seen River in two years and is worried. River has just woken from a seven month sleep and finds herself in the grip of Madame Kovarian. Post ATM. Includes: The Eleventh Doctor, River, Clara, Amy and Rory, Rose, Tenth Doctor Duplicate, Alt!Amy and Alt!Rory, Brian Williams, Madame Kovarian, and the Silence. 11/River, Rose/TenToo, Amy/Rory. Rotten Summary, I know
1. Chapter 1

**So I know I never finish anything so if you want to skip this story its fine but maybe fifth time's a charm? This story is River/Doctor (11) centric and involves a timebaby (of course!) but it's not fluff (hopefully). Anyways it also includes Clara, Rose and the Tenth Doctor's duplicate, Amy and Rory from both universes, Madame Kovarian, the Silence, and maybe Brian? Don't quite know yet. **

The Doctor flew around the Tardis controls, flipping off the breaks and using the stabilizers. The last thing he needed right now was to wake Clara up and be forced to have the where-are-we-going conversation which would ultimately force him to come up with a new destination.

The Tardis landed with a slight bump and the Doctor turned nervously towards the stairs. Such a bump would never have woken Amy or Rory but Clara was notoriously quick on her feet and a light sleeper. The door creaked open and River stepped through, a playful look on her face.

"Sweetie, what have I said about landing in the living room?" She was fully dressed, a gun in the holster around her waist despite the late hour.

The Doctor spun around to face her, "Well . . . "

"Don't. I hate looking for furniture." River pulled her blue diary out from under her arm and began to page through it.

The Doctor walked over and hugged her. Stunned, River returned a hug before pulling him away from her to look at him, "Post Manhattan?"

He nodded and turned away. The pair stood in a moment of awkward silence before he spun back around, an accusatory look on his face, "Where have you been?"

"What?" River didn't seem startled though, more resigned.

"I asked you to come with me and haven't seen you since. I found your address, I went to your house and when you weren't there I returned later and later but you never showed, until today!"

"Sweetie –"

"Where. Have. You. Been." It was not a question, it was a command. The Doctor glared at her, "This the first occurrence of you since Manhattan and it's been nearly two years for the Earth."

River just looked at him, silent before turning away, "New companion yet?"

The Doctor held his stare for a moment longer but when she refused to meet his gaze he shrugged, "Clara."

River gave a slight smile, "I always liked her though she did need a few friendly warnings."

The Doctor chuckled and turned away, back to the controls, "Naturally."

River walked up to him and put her hand over his, "I'm sorry."

He nodded but pulled his hand away. He threw a lever and the whole Tardis jolted, he didn't even remember that Clara was sleeping. And indeed, she wasn't. She'd heard the whole conversation.

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River woke up dazed and disoriented. The sterilized white of the surrounding room nearly blinded her as she regained consciousness. As the room came into focus she seized, prevented from any large movement by cuffs up and down her body. She wrenched against them, trying for calm, and a trickle of blood ran down her arm.

"Now, now, Melody." Madame Kovarian looked down at River, an expression of satisfaction on her face. "Try not to struggle, it's bad for you in so many ways."

River stopped pulling at the bonds but the panic behind her eyes was evident, "Let. Me. Go."

Madame Kovarian shook her head, "I'll let you up though." She flipped a switch and the table folded upwards. "I would have been more careful, if I were you and I definitely wouldn't have left the Doctor's side."

River glared at her but didn't answer with a usual retort. Madame Kovarian grinned and pressed a button on the wall, "We need to do some tests – you never know after all. Time lord biology is so tricky. It took a huge amount of resources for us to get your mother through the birth."

Shock blanked River's mind for a moment, surely not . . . but there it was. As she looked down she could see the pregnancy bump and she berated herself for being so stupid. She could remember finding out, it hadn't been that long ago – definitely not long enough for her to be this far along. Shuddering, River looked back to Kovarian, "How long have I been here?"

"Seven months." Kovarian patted River's stomach and River flinched. "I'll leave you to the doctor's now." She smiled and left the room.

Two humanoids walked in, a woman and a man, looking nervous. They'd been warned to an extent about this psychopath. According to their coworkers, she killed for sport and had even been locked away in Stormcage for it until she'd somehow managed to score a release. The last thing they wanted to do was be anywhere near her.

River's appearance startled them though. Her eyes weren't cold, her whole appearance didn't scream assassin or killer. To them, she looked defeated; her hair was straggling out of the bun she'd put it in seven months ago, her eyes were downcast, and blood was running down her arms from her attempt to get out.

The woman stepped forward first and, despite her confusion, reached out to River, "I'm Sabrina . . . I'm here to make sure the baby's healthy and to deliver it. Please feel free to ask me anything, Melody."

"My name isn't Melody." River refused to meet Sabrina's eyes, focusing instead on the cuffs which bound her to the table. She began to wriggle her arms around, testing the strength of the metal.

Sabrina looked down at her chart, the name there was Melody Pond. She turned to the man, "Do we have the right room?" She dropped her voice to a whisper, "She doesn't look like we were told."

The man nodded and stepped forward, "What is your name, miss? We mean no disrespect and we're sorry if you've been mistaken for Miss Pond . . ."

"No, you didn't just grab the wrong pregnant woman off of twenty-first century Earth. I'm River though, River Song. I don't go by Melody Pond, haven't for years." River looked up at him, "Do you think you could let me out?"

Sabrina reached for the controls but the man stopped her, "I'm sorry Miss Song, no. You can't be let out." He turned to Sabrina, "It's a trick."

River banged her head on the table, "It's not a trick. I'm pregnant and have been on this table for seven months. I'd like to move."

Sabrina turned to her coworker, "Damien, what are we going to do? Not let her move for another two months?"

"No." Madame Kovarian strolled in with a pair of soldiers, "See, I knew this would happen. I knew rumors would fly about _Melody._ And I knew that when you saw her, you would take pity."

"Ma'am . . ."

"No. Thank you." Madame Kovarian walked over to River and checked the bonds, "We needed to send her away and sooner rather than later. You just reminded me as to why. Not to mention that we don't want a repeat of last time."

Sabrina opened her mouth in confusion but Damien just shook his head, "What are we actually here to do?"

"Just give her these injections and leave." Madame Kovarian held up a box, "Check to make sure the baby's ok and then leave her with the guards. Here's the code for the cuffs, you wouldn't have been able to release her even if you wanted to." Madame Kovarian handed them a piece of paper, smiled at River, and left the room.

Sabrina opened the box of injections and paled. "Damien . . ."

He glanced over, the box was full; nearly twenty bottles of liquids to be inserted into the blood stream. River was looking at them almost nervously and, at the expressions on their faces, began to wrench at the cuffs.

The two doctors glanced from the pregnant woman to the guards before Damien sighed, "They could be good for her . . ."

Sabrina looked at him in disbelief, "You can't honestly think that."

River bit her lip, "What is it? Just tell me."

Sabrina handed the box to Damien and walked over to River. "I'm going to let you out now but . . . when I do; we'll also have to start giving you the medicine."

River nodded and Sabrina unlocked the cuffs. River slid off the table only to have her legs give out on her as soon as her feet hit the floor. She glared at the floor in irritation and struggled to stand. Sabrina tried to help her up but River just jerked away.

"Ma'am, Sir, Madame Kovarian orders you to begin. We will help if necessary." The soldiers moved to stand on either side of River, who immediately gave them an irritated look.

Damien shakily started to put the first vial into the injector, "River, can you stand up, please?"

"No." She tried again to make her legs work but they were simply too weak after months of malnourishment and being held in one place.

Damien looked to Sabrina for assistance but she shrugged. The soldiers, taking this for as a sign yanked River up with no care towards her chaffed arms. She gasped slightly in pain and Sabrina opened her mouth to demand the guards release her but Damien shook his head, "We can't administer these in any other way."

Sabrina sighed and began to line up the bottles in the correct order, trying hard not to look at River's increasingly pale face.

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On a misty beach in another universe a family was setting up a dinner – an age old tradition.

**Alrighty, this looks alright enough. And writing TV characters is hard! I feel like I did a terrible job with such complex characters . . . .Oh well . . . Please leave a review!**


	2. Chapter 2

**First Review! Yay! Thanks you! (I'm a little review crazy) Anyways, it may get a little confusing but remember that the River that's with the Doctor (right now) is the future version of the River who's with Madame Kovarian . . . probably should have made that clear. I can't think of anything else . . . besides the fact I don't like my OCs and I think all of the characters are OOC. **

Rose Tyler laid out a thick blanket, already cold, it was a shame her husband insisted on celebrating their anniversary here every year. They could be inside by a fire or just out of the wet. Bad Wolf Bay was always misty. But still . . . it was sweet of him. Wrapping her coat closer around her, she called out to her husband.

"John! Come on!"

John carried a little boy on his shoulders with curly blonde hair. Rose smiled and reached out to grab her son, "Look, its James first anniversary outing."

"He looks miserable." A woman with straight auburn hair with a tight hold on her three-year-old daughter walked over, "I can never understand why you two have your anniversary here."

Rose and John had never told anyone about where they came from or why they chose Bad Wolf Bay as their anniversary spot, best to keep that sort of thing within the family. Amy and Rory were their best friends, though, so they often considered telling them their whole story. Both worked as Torchwood as well so it would be believable but Rose and John had gone so long without telling anyone that it didn't seem realistic to tell anyone.

Rose shook the thought of telling them out of her head and took out the food – which was absolutely free of pears. She grinned inwardly at her husband's phobia. Amy and her daughter sat down smiling.

"Where's Rory?" John glanced around for a sign of Amy's husband.

"He has to work late . . . something about a rift being weak. It's not even his area." Amy frowned for a moment but changed the subject, "So, how's James?"

"Oh he's brilliant!" John grinned ecstatically and began to ramble about all of his sons accomplishments before Rose interrupted:

"Yes, dear. That's wonderful." She turned to Amy, "Sorry about all that. How's Melody?"

"No problem and she's great. Starting to want to do things for herself and such. Rory's losing it." Amy laughed, "I'm worried he'll smother her when she's a teenager."

The five chuckled, it was probably true – Melody was in for a rough ride, it would be a miracle if she got a boyfriend that stayed before she was twenty. Their conversation was brought to a sudden halt as a group of Torchwood cars appeared at the edge of the beach.

Amy leapt to her feet, holding Melody, at the sight of her husband running towards them. "Rory! What's happening?"

"C'mon! Get up!" He reached them panting, "A hole's opening! We don't want anybody pulled through or crushed by whatever's coming through!"

Rose gasped, a smile breaking across her face but John picked up James and began to rush off the beach, grasping Rose's hand, Amy, Rory, and Melody followed them

"John! What're you doing?"

He ground to a stop a safe distance away and turned to her, "Rory's right. A hole could open up that's so big that it could allow a building or army through. The hole is never supposed to open. It was sealed right and properly after the Medusa Cascade. The only way it could open is if someone over there was doing it purposefully."

Rose stared at the now rippling beach, "But what if the Doctor –"  
"Rose. He wouldn't. I'm sorry but he wouldn't."

"What are you two talking about?" Amy glared at her friends, still panting slightly from the run.

" I -"

"John!" The head of Torchwood, Jack Barrowman, strode over, "I need you experience, when whatever it is comes through there, I need you to tell us what to do and whether it's safe or not."

John nodded and the group looked at the spot anxiously. A bright light split the fabric between universes and a figure dropped through.

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"Doctor!" River grasped onto the control console in an effort not to fall over. "Where are we going?"

"I don't know." He still wouldn't meet her eye. "Wherever the Tardis thinks we should be."

River nodded and the only think to break the silence was the chaotic noise of the brakes – wait, the noise was nearly deafening, "Doctor!"

"Yes?"

"Where's Clara?"

The Doctor's cringed inwardly and thrust off the brakes. There was still no sound from Clara and she usually made herself known. River rolled her eyes, "Oh, Doctor . . . Clara?"  
Clara poked her head out from behind the wall, "Yes? And who're you?"

River sighed, "I'm River Song . . . I'm sort of – "

"My wife. I'm married." The Doctor glanced nervously at Clara, whose mouth was open in shock.

"Really? You're married?" Clara sized River up, trying to figure out what was so special.

River stared right back at Clara, arms crossed but there was laughter in her eyes. The trio stumbled as the Tardis landed with a jolt. It groaned, the light in the center flickering. The Doctor stroked it lovingly, "Oh, what have you done to youself?"

River went over to the console to inspect the readings but Clara simply walked to the door. "It looks like Earth – wait not quite. Doctor?"

River skimmed the readings and with each word her heart sank a little further. The Doctor glanced over her shoulder. "Brilliant! Good atmosphere, nice planet. Let's go!"

He grabbed River's hand and pulled her towards the door Clara had already gone through. Just short of the door, River snapped out of her daydream and pulled herself free, "I can't."

She stared out the door. All she could see was the metal of the military base that was dotted with rain. Her mind struggled to make sense of it all – it seemed like yesterday she was there but it was over a year ago. The Doctor was looking at her in confusion with a slight hint of anger. Of course he was angry; all she ever did was withhold information – things he needed to know.

"Sweetie . . . . You need to be here but I can't be." River backed away from the door slowly, staring as if the base were a weeping angel. When she reached the console she turned away. "I've got my vortex manipulator. I've got to go home."

River disappeared in a burst of light. The Doctor had tried to race back towards her to no avail. "No!" Anger laced his voice as he smashed his hands on the console which his wife had been standing in front of seconds ago.

"Doctor?" Clara reentered the Tardis. "Where'd River go? You know, the _wife_ you never told me about!"

"Gone . . . She's gone." The Doctor spun around and began to mutter to himself, "She never runs away . . . Why would River run? The last time was . . ." Realization dawned on his face. "No . . ."

The Doctor raced down the steps, grabbing Clara's hand, and out onto the base. It looked abandoned. He whipped out his screwdriver and began to scan for energy signals. Clara stood a few feet away, hands on her hips.

"Doctor, what the hell is going on?"

The Doctor flipped around, anger lacing his features. "I haven't seen my wife in two years! Missing for two years! When I do find her, she refuses to tell me where she's been and runs. River Song never runs. The last time she did was because it was the day she was born and kidnapped. She couldn't be there. Which is _exactly_ what she said today!"

Clara opened her mouth but closed it again, deciding it was best just to let him be. She glanced the area for any sign of anything. A flash of color caught her eye. "Doctor?"

"Yes?" He didn't really hear her though. The energy readings were far too high. For any base. He'd never seen one use this much energy. Not even at Demon's Run.

"I think I saw someone over there . . ."

He swung the screwdriver around, "Yes! Finally a bit of good fortune!"

As soon as they rounded the corner the woman screamed, "I'm sorry! Please don't kill me!"

The Doctor lowered the device, "Just us! Don't worry. What are you sorry for?"

Clara knelt beside her, "What's your name?"

The woman sat up, she was wearing a doctor's coat, "My name's Sabrina and I'm sorry . . ."

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John nodded and the group looked at the spot anxiously. A bright light split the fabric between universes and a figure dropped through. After the fall she didn't move. The soldiers stood at attention, guns poised and ready to fire but didn't really seem like they would. John rubbed his eyes, trying to erase the spots that had formed there. Jack staggered forward towards her.

"It looks like a woman . . ."

John made out the curly frame of hair surrounding her face. _Surely not . . ._ "Rory?"

Rory nodded and the three of them moved cautiously towards the woman with Rose, Amy, and the children close behind. John could see now. It was obviously her – River Song, the woman from the library. But she looked so different . . . younger and _pregnant_. He must have noticeably paled because Rose grasped his hand.

"Who is she?"

He looked at her "I met her a while back – with Donna. She died though . . . I guess it's in her future still . . . "  
"John, should I help her?" But Rory was already getting out his kit. He felt protective . . . He instinctively knew she was no threat.

John nodded but Jack looked uncertain, "Shouldn't we contain her first? Or-or run some tests or something?"

"No." John's voice was definite. There wasn't room for arguing. "Let Rory help her."

Rory knelt down and gently began to wipe some of the dust and debris from her skin. He turned over her arms and wiped them off. At the sight of them he paled, "John . . ."

"What is it?" John had been lost in memories of that fateful day in the library but when he looked down he felt sick. There were bruises up and down her arms which were dotted by injection marks.

Amy leant forward to see what they were talking about, as soon as she saw the damage she began to cry. Rose looked at her in concern and confusion but put a comforting arm around her, "Hey, it's alright . . . Do you know her?"

"No . . ." Amy turned away and buried her face in Rose's shoulder. "But . . . Oh, I don't know."

Rory sat back, "We should really run some chemical tests now . . . We have no idea what's been injected into her blood . . ."

At that moment the air began to shimmer again. An opaque image of a running woman appeared. Red hair masked her panicked face as she rushed over to the woman lying on the ground. "River! River, can you hear me?"

The group stared in shock as the woman then faded away. Rory turned to his wife and then back again to the woman, River, apparently. Amy stuttered, "That was _me._"

**Okay! Chapter two done! I've decided to update on Fridays, Saturdays, and Sundays although I'm not 100% sure about Fridays. Anyways, that should at least make sure I get three chapters up a week. Please leave a review!**


	3. Chapter 3

**Chapter Three! Writing as quickly as possible over here! **

"**Never ignore a coincidence – unless you're busy."**

River had really tried to end up in the right place, minutes after the Doctor took her away. But when had steering with a vortex manipulator worked out all that well? Particularly since she had been in the Tardis when she activated it. Sighing she glanced at her surroundings. Skyscrapers surrounded her but River was in an alley – dirty, grimy and nowhere near where she wanted to be.

She typed away at the vortex manipulator, resetting the coordinates but, upon finishing it simply sparked and the lights dimmed. _Of course . . ._ She'd tried so hard to escape this part of her past. The last thing River wanted to do was be responsible in any way for everything that had happened. Memories flashed back from that time – not happy ones either. River winced away from them and put a hand on the slimy wall to steady herself. Feeling slightly panicky she stumbled forward. If she could just get back to her house, she could just have been misplaced in location. Yes all she needed to do was get back home.

River tried to walk confidently out into the street to no avail. The memories were crushing her – it was becoming impossible to keep them at bay and her vision was blurring. She stumbled across the thankfully empty street and up some stairs. Reaching the top she fell against a door. A blue door . . .

"Yes?" Amy's hair was pulled into a bun and her clothes screamed 1940's. "River!"

"Mother . . .?" River stared at Amy, she must be hallucinating. "It's not possible . . ."

Amy knelt down to River, "Never mind that, are you okay?" She checked over her daughter for bumps and cuts. Finding none she pulled River up and drew her close, "Come inside, your father will be happy to see you."

River let Amy pull her into the warmly lit house but her mind and heart filled with dread. She wanted nothing to do with this. She didn't want to be on the other side and certainly not too soon. Amy pushed her disconnected daughter down on the couch, "RORY!"

"Yes? Amy are you alright – River." Rory rushed in, pulling a robe around his form. "How-How can you be here?"

"I haven't the faintest idea. . . But you two need to do something for me – past me." River met each of their eyes but rather than the glint of adventure that was usually present in hers there was only resignation.

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"Why are you sorry?" Clara helped Sabrina to her feet; taking in the woman's disheveled appearance.

Sabrina looked at the Doctor, "You're him, right? The Doctor?"

He nodded, trying to calm the tension rising within him, "Tell me, Sabrina. What happened?"

Sabrina winced, "There was this woman here. We were told she was a criminal, that she murdered good people for sport, that she deserved what was coming for her but –"

"Don't make excuses." The Doctor had processed the information of the last ten minutes at lightning speed. He knew River must have been there.

Sabrina looked down, "You're right. We could have said something or walked out, but we didn't. We did what Madame Kovarian asked –"  
"Madame Kovarian!" The Doctor blanched, "Tell me my wife's alive!"

"Doctor –" Clara tried to comfort the Doctor but he jerked away.

"Tell. Me. What. Happened."

Sabrina shrunk back, "We had to give her all these injections. Madame Kovarian said she needed them for the childbirth."

"Childbirth!" Clara exclaimed, she flipped around to face the Doctor who had stumbled against the wall; pale as a sheet.

"No . . . Not again . . ."

Sabrina started to cry, "I'm so, so sorry. I didn't mean any harm! I didn't even know she would be pregnant!"

The Doctor stood straight again, his eyes blazed with anger, "Do you understand what you have done. Tell me you understand that you injected a pregnant woman with possibly, probably, harmful drugs. Do you understand?"

"I-I'm sorry . . ."

"You're _sorry_? Where is she. Where is my wife?"

Clara, scared by this darker side to the man she'd grown to believe was always in the right, rushed to him, "Doctor, stop. She couldn't have known . . . And what could she have done? Nothing would be different."

He stared at her for a moment before turning away, his body deflating, "She was pregnant! I should have been there. I should have rescued her."  
"Doctor –"  
"No!" He faced her, guilt written across his face. "I didn't save her mother when this happened and now I haven't saved her!"

Sabrina coughed, "I don't know exactly where she is or what's happened since, but they took her to that warehouse over there and then they were all gone. I don't know –"

The Doctor took out his sonic, hoping, _praying _she was somewhere inside. But the screwdriver showed nothing. No energy signals. It was almost as if – a memory surfaced but he pushed it away.

"Clara." He gave her a quirky smile. "Ready for a trip?"

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The group stared in shock as the woman then faded away. Rory turned to his wife and then back again to the woman, River, apparently. Amy stuttered, "That was _me._"

Rose patted her arm in an attempt to comfort her, "John?"  
"She was bleeding through." He stuck out his tongue, "Metallic! Haven't seen this since you crossed! It's brilliant!"

Amy rolled her eyes; most of what John said went over her head. She knelt next to her husband, leaving Melody with Rose. She fixated on the woman who her other self had been so focused on. There was nothing all that remarkable about her – Amy didn't even recognize her as someone she'd ever seen but she did feel a link with her.

River stirred, her eyes opening blearily, "Mother?" She looked at Amy and smiled, "I knew you'd turn up . . . Knew the Doctor was wrong."

Amy sat back, shocked. She turned to her own daughter. Melody didn't look anything like the woman on the ground and yet there was a similarity. "Rory . . ."

"So you did find Rory . . . I'd always hoped you might." River smiled dreamily. Rory waved a hand in front of her face.

"Stay with me, stay with me." He tried to take another look at her arms but she flinched away, clarity entering her eyes as she sat up and surveyed the group.

"Where am I? Who are they?" River tried to stand but was still too weak – possibly even weaker now than before. She glanced over her parents, they looked quite a bit different as well – more innocent.

Amy gently reached out to River, "I'm Amy, this is my husband Rory –"

"I _know_ who you are!" River glanced at them uncertainly, "You do know who I am, right?"

"I'm sorry –"

River pushed herself backwards, "Where am I?"

Jack stepped forward, "You're trespassing on Torchwood land, a beach called Bad Wolf Bay. I'm Jack Barrowman and I run Torchwood. Those soldiers are my soldiers. These are our most important consultants on alien behavior, John Tyler and Rose Tyler. The little boy is their son. The woman you called 'mother' is Amelia, Amy, Williams and her husband is Rory Williams, our primary field doctor. The girl is their daughter. Who are you, where did you come from, and why?" His voice was steely; confusion was dangerous in a business like Torchwood.

River stared at him for a moment, "My name is River Song but I chose it. My real name is Melody Pond –"

Amy immediately went into defense mode, "How could she, how dare she –"

John held up a hand, "Let her finish, I think Rose and I have the missing pieces."

Amy stared at him, lost. But River looked at him and gasped, "What? Doctor –"

"No, I'm sorry, River. Duplicate." His face had pity written all over it and a bit of guilt which River dismissed.

"Alright!" She could handle Doctor duplicates, that was familiar material. Unlike her parents . . . She pushed that thought out of her mind and gave them a brilliant smile, trying to forget what she'd been through. River was, after all, brilliant at hiding the damage. She even managed to stand, shakily "I'd appreciate it if you'd all call me River. Seven months ago this woman kidnapped me. I didn't even know until today, I just woke up. Anyways, they gave me a bunch of medicine and now I'm here!"

Rory saw right through her, he saw the sadness in her eyes and the panic. Nobody could be fine under the circumstances she'd described and he'd seen all those injections marks. "River, how far along are you?"

She crumpled, right back into the sand. "I don't even know, seven months and two weeks? Eight months? I don't even know how this happened, I was _so _careful. I didn't plan pregnancy but I prepared for the chance . . . this shouldn't have happened."

Rose tried to go to her but John stopped her, "Let me."

He knelt down next to her, "River. It's not your fault that this happened but you need to understand, look at me. Good, now listen. You're in a parallel universe, one without the Doctor and one without whatever took you. Listen to me; we will take care of you. We will find out what they did to you and why you're here. When we do, we will send you back."

River stared at him, slightly lost but nodded. Jack threw a glare at John for making so many promises for a woman none of them knew. Amy looked back and forth from River to Melody at the sound of a 'parallel universe'. Feeling slightly woozy she picked up Melody and turned away.

**No cliffhanger, sorry about that. Sigh, this really isn't working out at all, their characters are just impossible! I have no idea how River would act in a situation like this at all! How strong would she be? How desperate? Not a clue. Also sorry about the slight ramble. So, what do you think? Is there ever really a story where they just escape at the beginning and it's all beautiful? Yeah. . . No. There's a lot more plot to come (Not just the Doctor rescuing River and her giving birth). **

**Please review!**


	4. Chapter 4

**Wow! I don't think I've ever gotten so many reviews so quickly! I LOVE you guys! And sorry about the breaks between scenes, I did have asterisk's there but they didn't show up. Thanks MonkeyMail for pointing it out, I will use some other something from now on. I'm also going to stick to my three chapters a week deal so that I don't lose interest by writing out all my creativity at once (plus there's school . . . blech)**

**Anyways! If you have any questions, PM me or leave a review, I will always reply (hopefully).**

**On with the story . . .**

The Doctor grabbed Clara's hand and pulled her towards the large concrete building. Memories flashed through his head. Amy disappearing under the angel's finger . . . River in the Tardis, pushing the memory away . . . Her meeting his gaze – he'd thought he'd seen something else, he should have asked . . .His mind flashed back further to Demon's Run . . . This whole situation reminded him of then . . . Amy's face; tear streaked and betrayed flashed through his mind . . .

Clara yanked on his hand, "Doctor! Wait!"

He stared at her; childish confusion lining his face. They were only a couple of feet from the door but Clara didn't seem to notice. She was staring at him intently, when she'd met him he'd been so cut off from everything. She'd simply assumed that everyone who mattered to him was gone and that all she'd have to do was help heal the wounds. Clara had never expected this out-of-control emotional Doctor who didn't even realize when he was stupidly risking his life.

He started to pull away, towards the door to God-knows-what. Clara stepped in front of him, "Doctor. Look at me." She snapped her fingers in front of his face, "Now usually I'm all for reckless. Usually we have some idea as to what we're getting into. Could we take it slower? Just this once?"

The Doctor forced his gaze away from the door to his companion, "What? No – um – yes. Of course. Silly . . . trying to fix . . ."

Clara ignored him, it was fairly normal for him to have these moments – he'd been like that since she'd first known him. She pulled him sideways, towards the concrete wall; earning a grunt of irritation. Clara almost chuckled; he always loved to be in control. She stifled it though at the sight of blue electricity running down the wall and pulled him back.

The Doctor looked at the electricity in alarm. "Clara get back – Clara!"

The building began to draw all loose objects towards it, practically collapsing on itself. The Doctor pulled Clara back, grabbing onto the iron fence surrounding the compound. "Clara, listen to me. Do not let go, under any circumstances. Do not let go."

Clara looked into his eyes – the eyes so full of pain – and nodded. She opened her mouth to ask the questions he avoided at all costs but the pull of the building increased, pulling their feet off the ground. It was all she could do just to hold on.

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Amy turned away, carrying Melody. Rory stared between Amy, Melody, and River; stunned but he did not run. Amy wanted to run. She wanted to run so far away from this mess. Parallel universes? How could that woman be Melody from another universe anyways? She was older than Amy, herself. Amy held Melody close, breathing in her young daughter and trying to ignore the similarities she was already beginning to see between the two.

Rose gave her husband an 'I'll harass you about this later' look and rushed off after Amy, "Amy! Just wait! Let them explain –"  
"I think I understand." Amy turned around, full of spirit, "That woman, who is older than me, is my daughter from a parallel universe, according to _your _husband. Tell me how that makes sense." Rose tried to get a word in but Amy cut her off, "It doesn't. You can't explain it and do you know why? Because it's not true."

Amy looked down, _it can't be true._ She tried to push the horrible thoughts of what must have happened away. She'd seen her parallel self and she was only slightly older than Amy was now. River was older than her mum, even in that place. That, clumped with the state and reactions of the parallel women, led her to only believe something must have gone terribly wrong –

"Amy!" Rory cried out in panic. River had fainted and was now shivering, her forehead burned when Rory touched his hand to it. Rory was quick to accept the events, his protectiveness as both a nurse and a father kicked in. Amy, torn between wanting to ignore River's existence and the possibility of her grown up daughter needing help, simply watched and her hold on Melody tightened.

John knelt down in concern, "We have to get her to the medical facility –now."

"Do you understand what you're asking? You want us to take a foreign – possibly alien – woman into the midst of Torchwood where she would be ideally placed to learn everything. All of our work to protect Earth could be destroyed because you want to save one woman!"

John stood, his eyes flashing dangerously, "It's you who doesn't understand. I've met her only once but she gave me every implication to believe that she is one of the most important people in the Doctor's future. There is a _very _high possibility that the child is his. Do you understand?"

Jack nodded, gulping almost nervously. The last thing he wanted was to be responsible for River's death if the Doctor found a way to come looking for her – which seemed increasingly likely. He shakily motioned for his men to bring a stretcher, "Rory, go with them and look after her. John, I want to see you in my office in an hour."

John breathed a sigh of relief before turning to Rose. Thankfully, she hadn't heard who River was in his mind. He dreaded to think of her reaction. The Doctor, her Doctor, having a child? Not something he wanted to sit through. And then there was Jack . . . He was going to have to tell them all. They knew about Rose, of course. And they knew he was from the other side but they didn't know he was a duplicate of the famous Doctor they'd heard so much about.

Rose looked to her husband, reading his expression. She gave Amy one last concerned look before running over to him, "You alright?"

He nodded, "I'm going to tell him I'm a duplicate."

"Why?"  
"I have too much knowledge that could be useful right now."

Rose wanted to ask who River was. She knew John had recognized her – he'd gone so pale after all but she held back, he seemed so lost in his memories. "John? We better get going. . . ."

John nodded, "I'll drive – and I'm so sorry. This was supposed to be our anniversary –"

"It's fine, James likes Torchwood anyways." Rose bounced the little boy up and down on her hip, "Don't you James?"

He rubbed his eyes and beamed, pulling a weak smile from John, "You're coming?"  
"Of course!" Rose looked at him, astonished, "I'm not just staying at home. I want to know what's going on as well."

Amy watched the couple walk off along with her husband and her alternate daughter. She wanted to rush after them. She had to know the truth. She had to see and hear it for herself. She looked down at her daughter, "Melody?"

"Mummy?" The little girl looked at her in concern, "Is she going to be ok?"

Amy nodded, "Of course . . . of course she will be. Hey, do you want to come with mummy to work?"

The little girl nodded somberly, even she seemed affected by the events. Amy took a breath, "Rose?"

The blonde woman turned back to her friend, trying to gauge her reaction to the events of the day now that she'd had enough time. "Yeah?"

"You're going to Torchwood, right?" Amy glanced at the hostile expressions of the soldiers that were still on the beach; making absolutely sure nothing terrible was going to burst into existence, "Can we come? They don't usually let us in the med car with Rory."

Rose nodded and whispered something in John's ear. He looked from her to Amy and nodded, "Come on, Amy!"

Amy rushed after them, hoping that everything was untrue.

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"Past you?" Rory and Amy looked at their daughter, scared.

"I can't tell you much of anything." River bit her lip, a sign of nervousness that was uncharacteristic of her, "You were surprised, and you were both there. I'm going to need you."

Amy wanted to press her for more information but held back, "Alright. How are we getting to wherever you are or were?"

Rory was lost and was about to say so when Amy elbowed him in the stomach, River noticed and smiled weakly. They were the same parents she remembered and she'd often worried about them and how they would cope.

"I'm not particularly certain –"

"Where are you?"

River smiled, emotions now fully hidden, "A parallel universe."

Amy stared at her, "A parallel – what?"

"Universe, it's really quite exciting. You'll get to see yourselves in another life. They'll need your help and expertise which, I guess, you'll get from me." River pulled herself off the wall she was leaning against and glanced at her Vortex Manipulator – of course.

"Alright!" River set the coordinates on the time traveling device, "You need to fade in and out of that beach, Amy. The TARDIS sees both the future and the past. When I tried to leave from within it, it sent me here and put just enough energy into my vortex manipulator for you to bleed through. Of course that means I'll have to think of a more permanent method . . ."

"Wait!" Amy grasped River's arm, "What beach? What are –"

"Mother, we don't have much time." River but the black band around Amy's wrist, "The power's fading. I promise I'll explain everything when you get back. We'll figure this out. Don't stop to question yourself or anyone you see. Make sure they know I'm your daughter."

"River! What –what is –" Amy disappeared as River pressed the final button on the cuff. Rory jumped.

"River! You can't do that –"

"She'll be back, Father." River said, more confidently than she felt.

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Amy materialized on a misty beach. She glanced around frantically and, upon see the huddled group she ran towards them, her hair covering her face. She reached her daughter, who was laying unconscious and _pregnant_ on the ground. Taking in the damage she shouted.

"River! River, can you hear me?" She reached down to shake her daughter but the beach faded from her sight. She did not see her apartment come back into view.

**Woah. Friday update time! I had serious issues with this chapter and writer's block because I don't want to use impossible solutions. I hope the Vortex Manipulator thing was reasonable (from a DW standpoint). Anyways, leave a review on what you think!**

**I may be unable to update on Saturday and Sunday because I will be in New York (I get to see Newsies! Yay! Super excited) but, as it's spring break for me I will make sure that by the time next Friday comes around there will be two more chapters and then three more next weekend.**

**Also, Youtube channel: user/TheStarShinesForever?feature=mhee **

**Just for fun if you wanted to check out some of my DW videos. **


	5. Chapter 5

**Hmmm, not sure where to go with this . . . And sorry for the lack of update! No battery power = no writing. Anyways . . . Back to Doctor Who (Seen the new trailer + clips yet?) super excited! Only 8 more days!**

**One other thing – I **_**just **_**realized that when River slaps the Doctor and storms out after he heals her hand it's because she's mad at herself because she let him 'see the damage' and (in her mind) it makes his healing her hand and 'wasting' his regeneration energy her fault because she knows he can't help it. **

**So, remember when I was writing a story? Well here you go . . .**

The world spun around Amy for a moment before it straightened out. She clasped her head; something must have gone terribly wrong. The scene around her was completely unfamiliar – no not unfamiliar. . . just distant. A horn honked and Amy spun around to see a car – a 21st century car – screeching to a halt inches from her.

Stunned, Amy raised a hand in apology and backed out of the road. She never thought she'd see the 21st century again. Didn't the Doctor say New York would be locked from time travel? She glanced down at the vortex manipulator River had said was full of energy – apparently enough to drag her through New York but why here? Amy had been with the Doctor long enough to know that this neighborhood wasn't a coincidence – and it was too familiar.

"Amy?" Brian's voice rang out, "It's you? Isn't it? But the Doctor said –"

She flipped around and tackled him in a hug, sobbing weakly. She was confused and after what she'd seen on the beach, scared. He patted her fiery head in confusion, "Where's Rory? Amy, has something happened?"

Amy looked at him, wondering if she should tell him and _what_. Her mind recoiled at the thought of having to go through the whole story so she simply said, "Rory's fine, he's still stuck. But I'm sure he'll turn up, there's no way he's leaving me here on my own. What exactly has the Doctor told you?"  
"Just that you two were stuck in the past in New York." Brian smiled, "Didn't seem too bad to me, you were alive and together, but he was torn up about it."

Amy sighed. The Doctor never made her life easier – he probably never thought Brian would need to know about River but he should have told him because Brian _deserved _to know. She inwardly cringed. Brian did deserve to know but maybe with happier news than this? Yes.

"Brian, do you have a way of contacting the Doctor?"

Brian could tell something was on Amy's mind, she was usually impulsive and sporadic but this time there was panic in her expression and she kept looking at him like she was pondering something. There was something he should know but didn't. Whatever it was, she'd hoped and probably still hoped the Doctor would tell him.

"I do have a number –"

"Great! C'mon!" She darted into the house, Brian always kept numbers on the fridge and the Doctor's number was no exception. Amy grabbed the phone and put her anxious mind to work by slamming the numbers with her fingers.

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The Doctor and Clara were sitting on the ground looking at a, quite literally, hole where the building had been. All the debris around them had been swept up and pulled who-knows-where. The Doctor was speechless; memories that he had kept under lock and key were resurfacing and dancing in front of his eyes.

"Doctor." Clara stood and took deep breathes, trying to throw off the feeling of panic was growing. She looked to the Doctor and nearly didn't ask; he was staring into space but his eyes held so much pain Clara was frightened. She was frightened _of _him. Who could possibly hold that much pain and when it was unleashed . . . She pushed the thought from her mind and knelt back down, lightly grabbing his arm, "Doctor?"

He shook his head, "Yes? Oh, I was daydreaming?" He looked at her and his eyes were clear – emotion hidden behind rickety walls, "Sorry 'bout that."

Clara tried to shake the now growing unease she was feeling, "What was that?"

The Doctor jumped up and waved his sonic screwdriver in a pattern around where the building had been. "A void just closed – powerful thing. It sucks most the matter around it in. Once inside it's nearly impossible to escape. It's a terrible place – boring too. Sure hope River didn't end up in there."

Clara could see the worry in his face as he turned to give her an unconvincing smile. She smiled back, "I doubt it." Clara wanted to say more but she had no evidence, no ray of hope that could convince him River wasn't stuck in the void.

He gave her a slight nod and turned back to scanning the area – more for something to do rather than to gather information. This whole situation seemed like a mesh between Demon's Run and Battle of Canary Warf and that frightened him. He would never let it show but he was frightened. And he knew that Clara could tell something was wrong – she was never this quite.

Clara was sitting on the clean ground, for the first time, the adventure had been full of laughs and joy; ending in triumph. This didn't feel anything like success. Yes, they were where they should be but . . . it was clearly wrong.

The ring of a cell phone jolted both out of their broodings. Clara jumped up and spun around. How could a phone be ringing? They were alone and surely any phone would have been disconnected or ripped from a wall by the pull of the hole. The Doctor smiled a real smile for the first time in what felt like hours.

"It's Brian!" He was giddy at the idea of his grandfather-in-law calling him. "Hello!"

"Doctor!" A Scottish voice shouted from the phone and the Doctor's smile dropped as his mouth opened in shock.

"_Amy?!_"

Clara just stood there stunned by all these unfamiliar names but she did know the name Amy. She had been the Doctor's last companion and, from what she could tell (which was hard as he kept so much from her), his family. She mouthed the name in shock at him and he nodded back. Hope lighted in his eyes and he smiled with more ecstatically than she'd ever seen. Ripples of jealousy went through her body but she pushed them away and smiled back.

"Doctor, we need you." She began to ramble but most of it broke up and was unintelligible.

The dark tone in her voice caused his eyes to narrow in concern, "Amy, stop. I can't understand – no, just wait. How are you calling from Brian's cell?"

"I'm not sure how but I'm back in the 21st century, River had this plan –"

"You're back!" The Doctor interrupted, missing the last phrase, "Where are you? We'll be there right away! Wait, I can guess! You're at Brian's! Ha! Be there in a sec!"

"Doctor! Wait –" But Amy was cut off as he snapped the phone shut.

"Doctor, what –" Clara looked at him in confusion.

"They're back!" He grabbed his new companion's hand and pulled her back towards the Tardis, "The Ponds, oh I can't wait for you to meet them it'll be _brilliant_!"

Clara tried to smile but could only manage a grimace; what if, now that his initial, _better_ companions were back from who-knows-where, he just cast her aside? She couldn't shake the thought from her mind. She didn't want to go back to normal life- she couldn't. He knew that, didn't he?

They reached the Tardis and the Doctor laughed, "Oh, good old – wait, no – _dependable_ sexy. Never get's pulled anywhere!" He crashed through the doors, Clara following slowly after him.

The Doctor flipped the levers for 21st century Earth, "Oh, my impossible Ponds. Always getting the best of me!" The room jerked and both Clara and the Doctor crashed to the floor.

"C'mon!" He rushed past Clara and out the door. His new companion leaned against the door and watched as her – no, _the_ Doctor embraced a woman in old fashioned clothing with flaming red hair.

He smiled into it and held her as if his life depended on it, tears of happiness rolling down his eyes, "_Gotcha_"

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"Shouldn't she be back now?" Rory stared anxiously at the area where his wife had been nearly three hours ago. River had turned away and sat down long ago – she knew Amy should have returned no more than thirty minutes since she'd left.

"She should be." River hit her head on her knees, "She should have been back – she was only there for a minute."

Rory shook his head, "How could you let this happen?"

"Rory, I –"

"Your own mother! And you couldn't be more careful?" He glared down at his daughter, "You weren't even sure, were you?"

River took a breath and looked up, "There was nothing I could do. She had to be there."

"Nothing ever just has to happen!" Rory spun around in frustration before his frame relaxed, "River, where is she?"

River pulled herself off the floor, "I don't know, I'm sorry, I just don't. All I ever planned was for her to bleed onto a beach called 'Bad Wolf Bay' in the parallel universe. I thought she'd come back here."

Rory saw the guilt in her expression – and the fear. Something fatherly kindled in him, it had always been dormant before, and he awkwardly pulled his daughter into a hug. He'd almost never held her – not when she was a baby, not when she was a child when they were growing up, not when she was a teenager breaking all the rules, not when she regenerated in Berlin, not when she'd nearly died saving the Doctor, not when she revealed her fear of not being recognized by the Doctor in the future, not even when she came to visit them to share a dinner now and then or to tell them that the Doctor was alive – and, he felt warm. He'd always wanted children; he'd never realized he already had one.

River was surprised, she'd never been close with her father but she returned the hug; savoring its uniqueness. She could feel his sympathy and, where anyone else would make her feel uncomfortable, she accepted it. She pulled away first and gave him a shy smile. The interaction had given her more strength than she'd had for nearly two years – two years she went to great lengths to never think about.

Rory braced himself to ask her the questions he knew she never wanted to have to answer, "River, what happened? What's happening?"

She sighed, "It's – I – I can't. It's well, you're part of it. I remember you."

"River, please tell me _something_." Rory implored her but she simply smiled sadly.

"I wish I could." River glanced down before swinging her head back up, "Wait! You need to get there and I can't spend the rest of my life in this time period. There'll be a way to get back and maybe Amy's already there – hang on a tick."

She rummaged in a small purse by her side, "If I can just . . ."

"What are you doing?" Rory bit his lip, trying to hide the hope growing inside him."

River looked at him, eyes sparkling, "If Amy could get out then maybe – _maybe_ we could get a message to the Doctor and he could get us out. I don't know if it's possible – and it might already be out of our hands but this might just work. Aha!"

She swept out a tiny little device and looked at it for a moment. "There we go! Hopefully he'll get it." Rory stared at her in confusion. "It's psychic. The Doctor gave it to me when I got out of prison – before Manhattan. I sent him the dates so, with some help from the TARDIS, he might just get here by tomorrow – if he can."

Rory grinned, a bit of the hope showing, "Brilliant!"

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The car ride to Torchwood was silent except for the occasional gurgle from James which was immediately shushed by Rose. Melody was unusually quiet for a girl of her age and she held onto her mother's hand with a viselike grip. Amy didn't complain, she just sat there looking straight ahead; trying to think of nothing.

Flashes of the Library blocked John's vision every few minutes and his knuckles were white as he grasped the wheel. Rose was quiet but he could hear her suspicions through the awkward silence of the car.

When the med car stopped, John nearly ran into it his mind was so otherwise occupied. The jolt slammed Melody and James together and James began to cry. As Rose comforted the little boy Amy grabbed Melody and pulled her out of the car.

John rushed to the med car and watched them pull River out, "How is she?"

Rory shook his head, worry knotting his forehead, "Not well, her temperature's far too high and the baby's in distress. I need to get her inside and x-rayed immediately so if you could –"

"Oh, yes. Of course." John jumped out of the way and looked on in concern as the team rolled her inside.

"Is she going to be ok?" Amy had snuck up behind him, Rose was still calming James down.

Surprised at the concern he heard in Amy's voice, John simply said, "I don't know . . . we don't know what was put in her . . ."

Amy nodded and a shudder rippled through her body. The marks on River's arms stood out clearly in her mind. She picked up Melody and rushed into the building after her husband. John watched her go, marveling at their acceptance. When he met River, he'd been unable accept that she even knew him and yet here were Amy and Rory; accepting (even if they didn't know it) that River was their daughter from a parallel universe.

Rose finally calmed James down and walked over to her husband, grabbing his hand, "John? Are you sure about this?"

He nodded, he was sure he was ready to tell Jack who he was exactly. He just wasn't sure he was ready for his past to become his present. John looked at his wife and their child, he didn't want his old life to come back; it would ruin the family. Clearly, he no longer had a choice; he wasn't allowed to run away.

"C'mon."

The trio silently walked through Torchwood to Jack's office, ignoring the panic as employees prepared for any situation that would arise within the next weeks. The door to the office was made of dark wood, impenetrable by screwdriver John noticed.

Jack was sitting in a swiveling chair, his face creased with concentration and stress as he read through a large pile of papers. When the group walked in he stood, "John, you have created more stress and work for me than I would wish on my greatest enemy. I'm sincerely hoping you have a very good explanation."

John spread his hands, "Ask whatever you want."

Jack looked at him, a little caught off guard – something about John's personality was somewhat different but he plowed on, "Who is that woman? You seem to know her, how is that?" Jack sighed, "I know I'll never ask the right questions, could you just tell me what I need to know?"

"I'm the duplicate of a Timelord called the Doctor. I was born in battle and left in the parallel universe because of both the genocide I committed during it and because of his love for Rose. River is a woman he met on a world called the Library. She sacrificed herself in the end to save over four thousand people. I have the same memories he has. The woman is River before the Library and probably the daughter of Amy and Rory on the other side; they were also his companions on that side as well." John looked at Jack, "That's all I know, I don't know why she'd here."

Jack stared at him, "You're the Doctor? Or-or some version of him?" John nodded slowly, waiting for the information to sink in, "Wait! On the beach you said that the baby was –"

"Sir! John!" Rory burst into the room, "You'll never believe what I found!"

**So, I did not succeed in my goal but hopefully this was somewhat worth the wait? Can I have some reviews? I need a little motivation and feedback on how the characters are acting. Canon? Completely noncanonical and a disaster? Anything helps (except wholly negative feedback without anything constructive). **


	6. Chapter 6

**Alrighty, continuing (as my videos are bugging me, I shall write). Below is a ramble which you are more than welcome to skip, I just needed it out of my system.**

***ramble* Oh! There's one quick little annoyance I've experienced recently – people seem to be **_**extremely**_** concerned about this whole 'Doctor's name' deal. I've seen quite a few posts and comments where people condemn the Steven Moffat Doctor Who area as ruining the series because of the possibility of the Doctor's name reveal. One: Steven Moffat has not ruined Doctor Who in any way, in fact I was getting bored with it before he came along with overarching plots. Two: Nowhere has he said he will reveal or even give the Doctor a name, in fact, in an interview he said he never would reveal the Doctor's name as it could never live up to the buildup and expectations of fans. Three: the BBC summary says the Doctor's secret will be revealed but it does **_**not **_**say the secret will be his name. And, personally, if his name is asked on the Fields of Trenzalore (Where no man can speak falsely or fail to answer) I believe he will whisper his name to River (which would also tie up that loose plot end and, since they're the whispering couple, we wouldn't know). And this was not meant, in any way, to offend anyone. *end of ramble***

**So, prequel came out today! Loved it (naturally) so cute! On with the story and thank you to all my wonderful reviewers, favoriters, and followers! The inspiration comes from you (since my muse is incredibly lazy).**

Clara tried in vain to contain her jealousy as she watched the Doctor embrace Amy. She'd never be that to him, she'd never be nearly as much to him as Amy was. She'd never have the chance, anyways. Clara bit her lip and turned away back into the TARDIS; the blue, metal surfaces which she'd always believed were cold and harsh now seemed like a comfort. Something she had that Amy didn't she thought selfishly.

The Doctor popped his head through the door, "Clara, what are you doing? Come on!"

He disappeared again and she sighed but followed him out. She pushed her unease down and walked confidently into a perfectly organized living room. The Doctor was looking at her with glee, so happy to have two companions with him.

"Amy, this is Clara. Clara you've heard about Amy." He looked eagerly between the two of them, expecting something of them no doubt.

Amy shook her head, a smile playing around her mouth at the sight of her childish Doctor. She held a hand out to Clara, "Hi." She wasn't greatly pleased at being replaced, but it was her who suggested that he not travel alone.

Clara smiled and briefly shook her hand. Amy ignored the curtness in the encounter and turned to the grinning man, "Doctor –"

"Oh, yes!" He shook his head at her, "How did you get here? It should have been impossible."

A darkness appeared in Amy's eyes and his smile dropped slightly, "River said something needed to happen." The Doctor looked down; he wanted to ignore all the foreboding and increasing terrible signs. "River said I needed to get to beach – in a parallel universe."

"Bad Wolf Bay." The Doctor whispered, worry casting a shadow over his face. He looked to Amy, "You've been there, haven't you? You know."

Amy's eyes widened in shock, "You knew? You knew she was pregnant?"

"I found out." He looked down at his feet, "We went to the place where they were holding her."

Clara walked to him and put an arm around his shoulders; glaring at Amy for ruining his mood. He was so rarely as happy as she'd seen him. Most of the time he was haunted or hiding his emotions, the Doctor Amy had known was different – more together, more stable. She smiled at him, "Doctor, this is good news. It means River's alive, she's not stuck in the Void."

The Doctor looked at her and he seemed just like a child, needing confirmation. Clara gave him a squeeze and he nodded; hope reentering his eyes.

Amy noticed the interaction and mentally kicked herself, she'd seen his face – his world – crumple as she disappeared into the past. She should have known he wouldn't be the same as he was before. She had unknowingly added to the pile of those he believed he'd killed that weighed so heavily on his hearts.

Brian, on the other hand, was completely confused by everything that was happening. The Doctor was a different man then the one who had stayed with Amy and Rory during the invasion of the small cubes. To add to his confusion, the Doctor was accompanied by a pretty brown haired girl who he'd never seen before and they were talking about a woman called River like they knew her well and yet he'd never heard her name.

"Um, Amy, Doctor." He interrupted the guilt ridden moment with his typical mix of assertiveness and confusion, "What is going on. Who's River?"

The Doctor snapped out of his sorrow, "You never told him?"

Amy looked down in embarrassment, "I thought you would."

"Wait, you know River too? How?" Clara stared at Amy, wishing for her memories so she'd have some clue as to what to do – some clue as to what was going on."

Amy exchanged a silent message with the Doctor before nodding in resignation; River was her daughter – Brian's granddaughter – he deserved to have her tell him, "Brian, Rory and I never wanted to tell about River because of what happened to her." Amy took a deep breath, "When we were traveling with the Doctor I was captured because I was pregnant. The baby was part Timelord and I named her Melody after Mels."

"I'm a grandfather?" Brian looked shocked and happy all at once, "Why didn't you ever let me see her? Where is she?"

Amy had so hoped he would just understand or guess, but his mind was working against the truth, "Brian, she was stolen. I had one month with her as a baby. Rory – Rory never even held her. She was brainwashed to be a weapon – to kill the Doctor."

Brian's face fell, "Brainwashed . . ."

"No, no!" Amy smiled at him, "She turned out fine, she grew up with us – she was Mels, Brian. But, she could regenerate and when she was killed by Hitler –"

"Wait, _what?_"

The Doctor laughed slightly and Amy shot him a glare, "Never mind that, but the woman she became was River – a River born to kill the Doctor. And I'm not going to go into it but, for now, all you need to know is that she worked against the people who wanted him dead and tore time apart to save him. They were married and now she's stolen, just like I was, and she's pregnant, just like I was."

Brian stared at her, "Have I ever . . . seen her?"

Amy shook her head, "I'm sorry, she only ever visited us sporadically. But if you ever saw a woman with extremely curly blonde hair leaving our apartment, that was her."

Brian nodded. He had seen that woman on multiple occasions but had never asked about her or so much as said hello. Guilt flooded his system; Rory had told him they were unable to have children but there had been something else his son had wanted to say. And Brian had cut him off, thinking he was sparing the pain and Rory had looked down and shook his head in defeat. In an effort to think about something other than the pain and guilt, his mind flashed back to Mels – to the first time he'd seen her:

_ The Williams were sitting down to dinner with little Amelia and her parents. Mrs. Williams had been looking to set this up for a while; the Williams were new in town and, so far, the only connection she'd managed to make was with Amelia's mother. She was so excited when the two families had agreed to sit down for dinner and even more thrilled when she learned Amelia was the same age as her shy son, Rory._

_ The conversation was normal; work, school, how everyone was doing. The food was normal; a simple barbeque and the two children were getting along wonderfully. Rory had even allowed Amelia into his room. The two were up there, playing when the doorbell rang. _

_ Brian Williams, still laughing at a retelling of one of Rory's clumsy moments, opened the door to a dark skinned girl. Her hair was a ratty mess and her clothes were torn but there was a huge smile on her face at the sight of him – and the two children behind who had crept down to see who was at the door._

_ "I was told I should come here to see the Williams and Ponds." Her voice was unusually mature for a child her age. "I'm Melody but I prefer Mels now." _

_ "Where are your parents, Mels?" Mrs. Williams had come up behind Brian, looking at the girl in concern. _

_ Mels bit her lip, "I made a mistake and got on the wrong bus, they won't be here for another few days."_

_ "Why'd you come here?" _

_ "I think they mentioned you guys a while ago although you don't really know them." She glanced down sheepishly. A very un-Mels thing to do, Brian thought, looking back. _

_ Mrs. Williams looked from the child to her husband, kindness in her eyes. "Why don't you come in, Mels?" _

Brian smiled at the memory, he couldn't have known then. Mels had bonded so quickly with Amy and Rory, even when they were unsure of her. She literally stuck to them like glue. Looking back on all the memories, he couldn't remember a time when he'd seen her parents. Mels had never even mentioned them. Whenever he asked, she'd simply seemed confused before stammering something about them being busy.

Clara simply stared at Amy. River was Amy's daughter? So the Doctor and the Ponds had really been family. This time she didn't feel jealousy in heart but sorrow and pity. None of them had had this easy and it wasn't getting better – clearly.

Brian turned to the Doctor, "You're my grandson-in-law?" He chuckled, "Never thought I'd live to see my granddaughter married, particularly since I thought I'd never have one."

Brian pulled the Doctor into a hug but Amy tapped her foot impatiently, "Doctor! Brian! Please, can we focus on finding my daughter?"

The Doctor pulled away and clapped his hands, "Alright! So, River gave you the Vortex Manipulator and it somehow had enough power to get you to the parallel universe – _ow!_"

"Doctor?" Clara snapped back to the moment, "Are you alright?"

"Yeah . . ." He retrieved the glowing psychic paper from his pocket and fumbled with it. "It's burning . . ."

He managed to open it only by dropping it on the counter and knocking over a lamp. Clara jumped, used to his clumsiness, and caught it before it could shatter. Amy rolled her eyes at him; the Doctor wasn't exactly the same person but he was still her Doctor. His mouth dropped open, but into a smile.

"Doctor? What is it?"

"Your daughter." He smiled at Amy, "She's decided she doesn't want to be stuck in New York."

Amy gasped, "You can get them out?"

Brian looked like he might cry, "Rory, River, they can come back?" He missed his family and he thought he'd be without them for the rest of his life. He couldn't help but hope with all his heart that they could come back.

The Doctor was full of hope as well but he was trying to keep it restrained – this day, there'd been too much loss and too many swings of hope followed by disappointment. He looked to the numbers, the exact date and time to land at, and thought back to Manhattan. What if he shattered the planet? He couldn't let this become a choice between family and the Earth – it wasn't, not yet he tried to assure himself. The timelines were so scrambled after all . . . The most he could hope was that, with time, the city was a safer place to land. He looked at Brian and Amy and knew one thing: he had to try.

The Doctor nodded and smiled, "Well, let's go."

The four of them darted into the TARDIS. Amy and Brian started at the inside, "Doctor? What happened!"

"Oh, remodeled." He smiled at them and darted around the console, flipping switches.

"Wha – "

The Doctor laughed over her and hit the final control, sending the group to the ground.

**Ok so my muse hates me and I facing serious writers block hence the short chapter and really only one scene. Sorry about that. Maybe my muse will come back later today and I'll write the rest of the chapter.**

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**Youtube Channel: user/TheStarShinesForever**


	7. Chapter 7

**Figured it out! The writer's block for this episode is as long/large as the Great Wall of China. Fortunately I've now got some solutions figured out such as what will happen in the two years and what the injections are. Hate to tease but I'm just so proud of myself. Unfortunately, with two scenes I'm going to have to come up with some new conflicts. **

**Oh! And I know that a reviewer figured out the title (it comes from A Good Man Goes to War: **_**'demons run but count the cost, the battle is won but the child is lost'**_**) and I just wanted to make it clear (for my peace of mind) that this story is not a copy of that episode in any way (except for the pregnancy/Madame Kovarian deal). **

**Thanks for your reviews!**

"Sir! John!" Rory burst into the room, "You'll never believe what I found!"

John spun around; there'd been nothing unusual about River from what he remembered of the Library. Rose looked at her husband, ready to glare at him for withholding information but he looked as confused as she did. He was keeping something from her; she knew he, as the Doctor, had known River and had seen her die but she didn't know . . . _something_.

Jack rolled his eyes, "Of course! Just come on in, this is just the head of Torchwood's office."

Rory just stared at him with a puzzled look on his face before Jack sighed, "What is it, Rory?"

The doctor pulled out papers lined with numbers, "Her biology – it's like nothing I've ever seen!"

"Really?" John's voice rose slightly in curiosity and – like his original – excitement.

"Look at the DNA." Rory pointed to a strand. There was something off about it but it took John a moment to realize what it was. It had been years since he'd seen a portion of DNA like that, well, he'd never seen DNA quite like that.

"No." But John's voice wasn't upset or in denial, just in shock. The 'no' was laced with happiness.

Rose couldn't see what was different about the DNA, but she'd never been a scientist. She hadn't even read the books John had pushed at her when he got bored. "John, what is it?"

He looked at her, mouth slightly open, "Timelord, Timelord DNA." A smile broke across his face, "Timelord, Rose! Do you know what this means!"

Rose shook her head, "How – John, how could she be part Timelord? You said you were the last – Ohmygod is she your daughter?"

Jack started and looked to John in confusion, "Wait you said –"

"I know what I said." He looked down, "No, Rose, she's not. I'm fairly positive that she's Amy and Rory's daughter –"

"Now, hang on." Jack snapped, "That makes even less sense than your 'she's his wife –"

"_What?!" _

John winced and glared at Jack but before he could answer Rose's exclamation, Rory jumped in, "We could just, you know, ask her."

"She's awake? And you never thought to mention that before?"

Rory shrugged, "I woke her up with a bit of adrenaline, it was too dangerous for her to be asleep. Amy's with her now, it's a bit awkward, neither of them will so much as look at each other."

Jack nodded, "Let's go, and John – I still call you John, right? – John will do the talking. He knows her the best. Well, he's the only one who knows her."

The group walked the hallways in silence, Rose glaring a John until they reached the door.

"I'm not jealous or anything but how could you not tell me!" She blocked the door with determined look on her face.

"You want to discuss this _now_?"

"The Doctor has a wife he never told me about and she's inside right now. So, yes, now is the perfect time!"

John glared at her, "I don't know."

"What?"

"I don't know that she is his wife. I said it was likely just to shut these idiots up." He gestured to Jack and Rory who gave cries of anger and irritance. "Oh, don't worry I didn't lie. She could be – I don't know, I simply don't. But if we could just _talk_ to her." He looked pointedly at Rose who moodily removed herself from the door to go pick up James, who was supporting himself on the wall.

The group, less than happy stormed through the doors, earning a fiery glare from Amy, "What're you lot doing?"

River didn't so much as look up, she was too busy staring at her stomach; torn between worry and fascination. How many times had she hoped she would one day have a child? She'd never intended to bring one into her and the Doctor's hectic life but it existed anyway. When she finally did look up, she laughed a little:

John, who reminded her so much of her Doctor, looked at her like she was fragile, like she might break. He displayed the nervousness that a tell-tale trait of the younger versions of his original.

"Sweetie, I'm fine. I'm not going to break if you look at me." She smiled at him and gestured to the seat next to Amy; who was determinately staring at a reading on one of the screens – a reading she couldn't possibly read.

John sat on the chair, trying in vain to ignore Rose's glare – which had deepened at the term 'sweetie'. "River, I'm sorry but I'm not him."

River looked at him, at his eyes, for a moment, "No, you're not. I can tell." She sighed, "Wishful thinking. So, what is this place?"

John was surprised by her acceptance, it seemed unnatural, inhuman. She was, from what he knew, a time traveling archaeologist from the 51st century though. "You're on a parallel universe. It has several key differences but the most important one for you to know is that the Doctor doesn't exist in this world. Neither do his enemies, though."

River nodded but she didn't feel any safer. She'd been sent to a place where the Doctor's enemies didn't exist by the Doctor's enemies? There was something off about that but she tried to force all the flashing morbid thoughts from her head. She tried to find something else to focus on and her gaze landed on her arms. River looked from them to the – John.

"What, what did they . . ." She simply gestured to them.

John looked at her arms in worry before turning to Rory, who stepped forward. "River, we don't know. I'm sorry; I've tested your blood half a dozen times. The systems don't recognize the chemicals. The blood samples were sent to a lab but I doubt -"

She nodded, "It's ok. We'll find out eventually, some way or the other." River looked at her father; he seemed so young, so innocent, "You're from here, aren't you? Amy and the little girl – she's Melody?"

Rory thought he saw a sadness flash through her eyes and something else lingered in her expression – it looked like _envy_, "Are you Amy and my daughter? Over there?"

She flashed him a smile, "Spoilers."

"What?"

"You came in here for something. What was it?" River looked away from the parallel version of her father; there weren't really any secrets that needed hiding. She should tell them but she didn't want to – it was hard enough when her actual parents didn't recognize her but to have people who looked like her parents but weren't and never would be – it felt like it would kill her.

Jack stepped forward, "Ah, yes. We wanted to know about you Timelord DNA and who you are to the Doctor."

River nodded, "I have Timelord DNA because I was conceived in the TARDIS. As for who I am to the Doctor, I really don't know."

"Does anyone know!" Rose threw a hand up in frustration. John sent her a warning look but she continued, "Seriously? No one knows?"

River looked at her, "You're Rose?" She smiled, "Oh, dear, nothing is simple with the Doctor. He's not like us, he doesn't think like us. I _can_ tell you; this baby's his."

Rose's mouth dropped open in shock. The Doctor's child . . . he . . . she . . . Rose tried to keep the tears from her eyes. She loved John, it was true. She loved him more than she'd ever been able to love the Doctor. But the part of her that missed the traveling and wonder – the part of her that had loved the Doctor beyond reason – felt betrayed.

John looked guiltily at Rose, his heart – his human heart – breaking a little at the sight of her watering eyes. He wasn't enough. He'd never been enough for her – she still loved the Doctor, she always would. More than him. He looked back to River who was also slightly unnerved by the tears in Rose's eyes. John wanted to hate her for bringing the Doctor back into their lives – for tearing them apart but he couldn't. He just couldn't.

Jack broke the silence, "John, Rose, do you want to . . ." He motioned to the door but both of them shook their heads. They were going to have to talk but neither of them wanted to – not now.

Rory was still slightly bothered by the fact she'd never answered his question, "River, on the beach you thought we were your parents . . ."

River turned away, "Well, I was wrong. I didn't know where I was."

Amy finally pulled her stare from the wall, "River." She took the woman's hand awkwardly.

River looked at Amy, searching her eyes, "I'm your daughter – yours and Rory's – but not this you."

Amy nodded, "We look like them, but we're not. It's ok . . . hey, it's ok." She looked at John, Rose, and Jack and, to her, they seemed selfish. They weren't alone in a parallel universe – stuck, without their family and pregnant after being captured.

Rory half wanted to laugh at Amy's expression and half wanted to run and hide. Everyone simply looked away from the mother, abashed.

**Just needed to finish this phew, done. That was rough and more of a filler. Next chapter will be up Friday!**

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